Chchd1 (coiled-coil-helix-coiled-coil-helix domain containing 1) - Rat Genome Database

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Gene: Chchd1 (coiled-coil-helix-coiled-coil-helix domain containing 1) Rattus norvegicus
Analyze
Symbol: Chchd1
Name: coiled-coil-helix-coiled-coil-helix domain containing 1
RGD ID: 1307134
Description: Predicted to be involved in mitochondrial translation. Predicted to be located in cytosol and fibrillar center. Predicted to be active in mitochondrion and nucleoplasm. Orthologous to human CHCHD1 (coiled-coil-helix-coiled-coil-helix domain containing 1); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 2,6-dinitrotoluene; 3-chloropropane-1,2-diol.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: coiled-coil-helix-coiled-coil-helix domain-containing protein 1; LOC361005; small ribosomal subunit protein mS37
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8153,641,973 - 3,643,155 (-)NCBIGRCr8
mRatBN7.2153,592,719 - 3,593,901 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl153,592,727 - 3,593,901 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx153,602,910 - 3,604,092 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0154,989,386 - 4,990,568 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0153,601,719 - 3,602,901 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0154,025,455 - 4,026,637 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl154,025,463 - 4,026,637 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0158,126,673 - 8,127,855 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4153,818,169 - 3,819,351 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1153,818,167 - 3,819,345 (-)NCBI
Celera151,000,284 - 1,001,466 (+)NCBICelera
Cytogenetic Map15p16NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
2. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:12477932   PMID:18614015   PMID:22681889  


Genomics

Comparative Map Data
Chchd1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8153,641,973 - 3,643,155 (-)NCBIGRCr8
mRatBN7.2153,592,719 - 3,593,901 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl153,592,727 - 3,593,901 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx153,602,910 - 3,604,092 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0154,989,386 - 4,990,568 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0153,601,719 - 3,602,901 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0154,025,455 - 4,026,637 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl154,025,463 - 4,026,637 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0158,126,673 - 8,127,855 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4153,818,169 - 3,819,351 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1153,818,167 - 3,819,345 (-)NCBI
Celera151,000,284 - 1,001,466 (+)NCBICelera
Cytogenetic Map15p16NCBI
CHCHD1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381073,782,048 - 73,783,652 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1073,782,047 - 73,783,652 (+)EnsemblGRCh38hg38GRCh38
GRCh371075,541,806 - 75,543,410 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361075,211,834 - 75,213,137 (+)NCBINCBI36Build 36hg18NCBI36
Celera1068,824,977 - 68,826,575 (+)NCBICelera
Cytogenetic Map10q22.2NCBI
HuRef1069,536,882 - 69,538,480 (+)NCBIHuRef
CHM1_11075,823,585 - 75,825,183 (+)NCBICHM1_1
T2T-CHM13v2.01074,653,448 - 74,655,052 (+)NCBIT2T-CHM13v2.0
Chchd1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391420,753,095 - 20,754,493 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1420,753,074 - 20,754,493 (+)EnsemblGRCm39 Ensembl
GRCm381420,703,027 - 20,704,425 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1420,703,006 - 20,704,425 (+)EnsemblGRCm38mm10GRCm38
MGSCv371421,522,249 - 21,523,647 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361419,491,621 - 19,492,969 (+)NCBIMGSCv36mm8
Celera1417,085,793 - 17,087,241 (+)NCBICelera
Cytogenetic Map14A3NCBI
cM Map1411.53NCBI
Chchd1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495543718,116,923 - 18,118,670 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495543718,117,090 - 18,118,586 (-)NCBIChiLan1.0ChiLan1.0
CHCHD1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2885,932,917 - 85,934,259 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11085,938,245 - 85,939,583 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01070,304,964 - 70,306,299 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11072,977,573 - 72,979,166 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1072,977,573 - 72,979,166 (+)Ensemblpanpan1.1panPan2
CHCHD1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1424,217,363 - 24,218,739 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl424,217,433 - 24,218,739 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha424,355,007 - 24,356,330 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0424,497,771 - 24,499,094 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl424,497,788 - 24,499,094 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1424,394,926 - 24,396,247 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0424,595,347 - 24,596,670 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0424,950,398 - 24,951,721 (+)NCBIUU_Cfam_GSD_1.0
Chchd1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440721356,873,209 - 56,874,799 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365215,365,939 - 5,367,511 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049365215,365,934 - 5,367,514 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CHCHD1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1476,507,318 - 76,509,241 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11476,507,297 - 76,509,260 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21482,633,955 - 82,635,897 (+)NCBISscrofa10.2Sscrofa10.2susScr3
CHCHD1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1957,589,273 - 57,590,597 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl957,589,462 - 57,590,554 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366604818,166,402 - 18,167,721 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Chchd1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247547,297,531 - 7,299,058 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046247547,297,495 - 7,299,058 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Chchd1
3 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:32
Count of miRNA genes:29
Interacting mature miRNAs:32
Transcripts:ENSRNOT00000012372
Prediction methods:Miranda, Rnahybrid, Targetscan
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1354657Despr13Despair related QTL 130.0022locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)15129912054Rat
8552920Pigfal8Plasma insulin-like growth factor 1 level QTL 83blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)15134723002Rat
8694361Abfw6Abdominal fat weight QTL 610.20.001visceral adipose mass (VT:0010063)abdominal fat pad weight to body weight ratio (CMO:0000095)15134723002Rat
9589149Insul29Insulin level QTL 299.060.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)15134723002Rat
731170Pur3Proteinuria QTL 32.30.0005urine protein amount (VT:0005160)urine protein excretion rate (CMO:0000759)15141686771Rat
1641887Alcrsp14Alcohol response QTL 14response to alcohol trait (VT:0010489)brain neurotensin receptor 1 density (CMO:0002068)15142356671Rat
2298549Neuinf12Neuroinflammation QTL 123.5nervous system integrity trait (VT:0010566)spinal cord beta-2 microglobulin mRNA level (CMO:0002125)15155302115Rat
10401805Kidm51Kidney mass QTL 51kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)1530632945306329Rat
5684946Bss98Bone structure and strength QTL 983.90.0026tibia strength trait (VT:1000284)tibia ultimate force (CMO:0001734)15105825014481294Rat
1641913Colcr2Colorectal carcinoma resistance QTL 26.570.0197intestine integrity trait (VT:0010554)colorectal tumor number (CMO:0001794)15226636822711984Rat
1641913Colcr2Colorectal carcinoma resistance QTL 26.570.0197intestine integrity trait (VT:0010554)poorly differentiated malignant colorectal tumor number (CMO:0002076)15226636822711984Rat
738017Hcas7Hepatocarcinoma susceptibility QTL 72.91liver integrity trait (VT:0010547)liver nonremodeling tumorous lesion volume to total liver volume ratio (CMO:0001464)15226636846921453Rat


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 3 43 57 41 19 41 8 11 74 35 41 11 8
Low
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000012372   ⟹   ENSRNOP00000012372
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl153,592,727 - 3,593,901 (-)Ensembl
Rnor_6.0 Ensembl154,025,463 - 4,026,637 (-)Ensembl
RefSeq Acc Id: NM_001108369   ⟹   NP_001101839
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8153,641,973 - 3,643,155 (-)NCBI
mRatBN7.2153,592,719 - 3,593,901 (-)NCBI
Rnor_6.0154,025,455 - 4,026,637 (-)NCBI
Rnor_5.0158,126,673 - 8,127,855 (-)NCBI
RGSC_v3.4153,818,169 - 3,819,351 (-)RGD
Celera151,000,284 - 1,001,466 (+)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_001101839 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAI68773 (Get FASTA)   NCBI Sequence Viewer  
  EDL86243 (Get FASTA)   NCBI Sequence Viewer  
  EDL86244 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000012372
  ENSRNOP00000012372.4
Reference Protein Sequences
RefSeq Acc Id: NP_001101839   ⟸   NM_001108369
- UniProtKB: B5DER5 (UniProtKB/TrEMBL),   A6KKP9 (UniProtKB/TrEMBL),   F7ES83 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000012372   ⟸   ENSRNOT00000012372
Protein Domains
CHCH

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-B5DER5-F1-model_v2 AlphaFold B5DER5 1-118 view protein structure

Transcriptome

eQTL   View at Phenogen
WGCNA   View at Phenogen
Tissue/Strain Expression   View at Phenogen

Promoters
RGD ID:13699560
Promoter ID:EPDNEW_R10083
Type:multiple initiation site
Name:Chchd1_1
Description:coiled-coil-helix-coiled-coil-helix domain containing 1
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0154,026,633 - 4,026,693EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1307134 AgrOrtholog
BioCyc Gene G2FUF-14559 BioCyc
Ensembl Genes ENSRNOG00000009297 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000012372 ENTREZGENE
  ENSRNOT00000012372.5 UniProtKB/TrEMBL
InterPro CHCH UniProtKB/TrEMBL
  CHCHD1 UniProtKB/TrEMBL
  Cys_alpha_HP_mot_SF UniProtKB/TrEMBL
KEGG Report rno:361005 UniProtKB/TrEMBL
NCBI Gene 361005 ENTREZGENE
PANTHER COILED-COIL-HELIX-COILED-COIL-HELIX DOMAIN-CONTAINING PROTEIN 1 UniProtKB/TrEMBL
  PTHR31278 UniProtKB/TrEMBL
Pfam CHCH UniProtKB/TrEMBL
PhenoGen Chchd1 PhenoGen
PROSITE CHCH UniProtKB/TrEMBL
RatGTEx ENSRNOG00000009297 RatGTEx
Superfamily-SCOP SSF47072 UniProtKB/TrEMBL
UniProt A6KKP9 ENTREZGENE, UniProtKB/TrEMBL
  B5DER5 ENTREZGENE
  F7ES83 ENTREZGENE, UniProtKB/TrEMBL
UniProt Secondary B5DER5 UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-04-30 Chchd1  coiled-coil-helix-coiled-coil-helix domain containing 1   Chchd1_predicted  coiled-coil-helix-coiled-coil-helix domain containing 1 (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-12 Chchd1_predicted  coiled-coil-helix-coiled-coil-helix domain containing 1 (predicted)      Symbol and Name status set to approved 70820 APPROVED